README.md

In jmstrat/NMR.Utils: Importing and processing Bruker NMR data

NMR.Utils

Contains functions to automatically import, process and plot Bruker NMR data. Primarily designed to speed up the processing of in-situ electrochemical experiments.

Installation

1. Install the devtools package if you do not already have it:

install.packages("devtools")

1. Install this package

devtools::install_github("jmstrat/NMR.Utils")

Details

Graphical interface for in situ data processing

This package includes a graphical interface for importing, processing, and plotting in situ / operando NMR data. This processing wizard can be summoned using the incantation insitu_gui().

Importing NMR data

Use the function read.nmr to import 1D or 2D nmr data. Only processed bruker data (1D / 2D binary files), or files exported from topspin (convbin2asc / totxt) are supported.

Use plot or iplot to plot the data.

Scripting interface for in situ NMR data

• Import the NMR data using read.nmr; import the echem data using read.echem from the Echem.Data package.

• Set the time for each scan using storeOffsets. These times can be automatically generated from an ATMC log file using read.ATMC or without a log file using noATMoffsets.

• Combine the NMR and echem data with associate_echem_with_nmr.

• If complex, data can then be phased (apkpseudo2d), and made real (makeReal).

• Baseline subtraction can be performed using make_background OR correct_baseline

• Use plot to plot the data – see ?plot.nmr2dinsitu.data.object for options.

Any / all of these steps can be performed graphically using the command insitu_gui or any of the interactive family of commands (interactiveImport, interactivePhase, interactiveBaseline and interactivePlotting). Data can be exported as a csv file using the export function.

Fitting in situ NMR data

Import and process the data as described above. Note that it is very important that the baseline is 0 for fitting, if your baseline is reasonably flat the command data = correct_baseline(data, method="modpolyfit",degree=1) will fit a straight line to the data. Otherwise consider using interactiveBaseline.

• Create a fit object using new_fit, e.g. fit = new_fit(integration_range=c(-50, 50))

• Create one or more peaks using new_model, e.g.: electrolyte = new_model(pseudoVoigt, height=1e6, centre=0.2, hwhm=2.0, shape=0.5)

• Define which parameters of the model will be fitted using add_constraint_to_model, e.g.: electrolyte = add_constraint_to_model(electrolyte, parameter='height', constraint_type='vary', constraint=1e5)

• Add each model to the fit using add_model_to_fit, e.g.: fit = add_model_to_fit(fit, electrolyte)

• Run the fit using run_fit_for_data.

Results are available in the fit object under result, e.g. fit$result. These can be exported to a csv file using export. A simple plot can be made using plot(fit), or an animation as described below.

Animations

A simple animation of in situ NMR data can be made using save_animation, optionally including a fit.

License

This project is licensed under the GNU Affero General Public License v3.0 - see the LICENSE file for details

jmstrat/NMR.Utils documentation built on July 14, 2019, 11:35 p.m.